Project Viva: Age 7 DNAm and metals EWAS

Required Packages and functions

# libraries
library(sas7bdat)
library(sva)
library(reshape)
library(ggplot2)
library(gridExtra)
library(knitr)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(minfi)
library(stringr)
library(limma)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(minfi)
library(DMRcate)
library(UpSetR)
library(reshape)
library(corrplot)
library(factoextra)
library(ENmix)

# loading annotation
anno = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
anno = data.frame(anno)

# loading functions
setwd('/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local')
source('EWAS functions.R')

Load DNAm and pheno data

load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/Age7Blood_ComBat_Betas_Mvals_filteredProbes_metalAnalaysis.RData")

dim(pDatAge7Metal)
# 333 164

dim(ComBat.Mvalues.Metals)
# 394460    333

rownames(pDatAge7Metal) = pDatAge7Metal$samplename

pDatAge7Metal$age_yrs_7y_blood = pDatAge7Metal$c_age_days_7y_blood/365

EWAS

As

DMP_As = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  23361 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15951 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9103149 
 
# Number of DMRs identified:   5 

# rm(DMP_As); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
2	113992761	113993313	0.00e+00	552	0.00e+00	0.0000000	8
3	46759437	46759698	0.00e+00	261	0.00e+00	0.0000006	7
17	1395863	1396123	0.00e+00	260	0.00e+00	0.0000023	5
1	228395755	228396009	0.00e+00	254	0.00e+00	0.0000061	4
17	75315562	75315667	2.65e-05	105	2.65e-05	0.0947026	3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As/As_log2_manhattan_DMP_adj.png")

As, female

pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))

DMP_As_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  26064 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  15824 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9007317 

# Number of DMRs identified:   4 

# rm(DMP_As_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
1	11561496	11561711	0.0e+00	215	0.0e+00	0.0000021	3
7	76027000	76027101	0.0e+00	101	0.0e+00	0.0000095	3
2	113992842	113993142	0.0e+00	300	0.0e+00	0.0000303	5
2	198651075	198651347	6.4e-06	272	6.4e-06	0.0092121	3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F/As_log2_manhattan_DMP_adj.png")

As, male

pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))

DMP_As_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  11497 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14046 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8408844 
 
# Number of DMRs identified:   6 

# rm(DMP_As_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	47091977	47092178	0.0000000	201	0.0000000	0.0000001	4
2	164204627	164205032	0.0000000	405	0.0000000	0.0000038	5
17	1395863	1396123	0.0000000	260	0.0000001	0.0000717	5
16	88706240	88706389	0.0000016	149	0.0000024	0.0042168	2
8	22735275	22735388	0.0000089	113	0.0000107	0.0305879	3
7	27183400	27183436	0.0062439	36	0.0062439	1.0000000	2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M/As_log2_manhattan_DMP_adj.png")

Ba

DMP_Ba = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  11801 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11716 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7753982 
 
# Number of DMRs identified:   3 

# rm(DMP_Ba); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	6899084	6899577	0.0000000	493	0.0000000	0.00e+00	10
16	1583809	1584118	0.0000000	309	0.0000000	2.64e-05	6
6	32145616	32145626	0.0436714	10	0.0436714	1.00e+00	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba/Ba_log2_manhattan_DMP_adj.png")

Ba, female

DMP_Ba_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  29651 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  24029 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.224716 
 
# Number of DMRs identified:   5 

# rm(DMP_Ba_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	6899084	6899577	0.0000000	493	0.0000000	0.0000000	10
2	183943387	183943551	0.0000000	164	0.0000000	0.0000270	5
17	37123637	37123949	0.0000000	312	0.0000000	0.0000168	9
7	94285269	94285352	0.0000006	83	0.0000008	0.0029480	7
11	111250128	111250201	0.0009145	73	0.0009145	0.9928711	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F/Ba_log2_manhattan_DMP_adj.png")

Ba, male

DMP_Ba_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  25363 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  26609 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.225518 
 
# Number of DMRs identified:   3 

rm(DMP_Ba_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
16	1583809	1584118	0e+00	309	0e+00	0.0000000	6
19	50194119	50194252	0e+00	133	0e+00	0.0000052	5
6	29595001	29595335	1e-07	334	1e-07	0.0001322	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M/Ba_log2_manhattan_DMP_adj.png")

Cd

DMP_Cd = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  9428 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11856 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.8163213 
 
# Number of DMRs identified:   4 

# rm(DMP_Cd); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
112561	cg07044523	0.2554657	0.1719724	0.3389591	5.275559	6.019999	0	0.0019081	10.31706	0.0019081	0.042597	chr1	153514376	S100A5	153514376

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
7	158045979	158046166	0.0000000	187	0.0000000	0.0000093	3
5	23507449	23507656	0.0000000	207	0.0000000	0.0000228	5
17	46685291	46685448	0.0000000	157	0.0000001	0.0001083	5
7	27184158	27184188	0.0027811	30	0.0027811	1.0000000	4

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd/Cd_log2_manhattan_DMP_adj.png")

Cd, female

DMP_Cd_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  13276 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  13473 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8343739 
 
# Number of DMRs identified:   7 

# rm(DMP_Cd_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	32164926	32165321	0.0000000	395	0.0000000	0.0000000	7
17	46685291	46685448	0.0000000	157	0.0000000	0.0000007	5
1	26233403	26233623	0.0000000	220	0.0000001	0.0000554	8
6	1624385	1624442	0.0000001	57	0.0000001	0.0004341	2
5	23507449	23507656	0.0000001	207	0.0000001	0.0001299	5
11	73357094	73357276	0.0000022	182	0.0000025	0.0046583	6
5	132113754	132113860	0.0159548	106	0.0159548	1.0000000	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F/Cd_log2_manhattan_DMP_adj.png")

Cd, male

DMP_Cd_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16666 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  19722 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.070021 

# Number of DMRs identified:   3 

# rm(DMP_Cd_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	61446961	61447369	0.00e+00	408	0.00e+00	0.0000000	11
7	50518572	50518647	1.70e-06	75	2.60e-06	0.0090132	2
6	28446839	28447087	5.55e-05	248	5.55e-05	0.0844649	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M/Cd_log2_manhattan_DMP_adj.png")

Cr

DMP_Cr = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  29723 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23497 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.107048 
 
# Number of DMRs identified:   5 

# rm(DMP_Cr); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
5	145758709	145758881	0.00e+00	172	1.00e-07	0.0000526	4
16	66969473	66969500	0.00e+00	27	1.00e-07	0.0003537	2
6	33245769	33245895	8.00e-07	126	1.40e-06	0.0025854	6
19	50666378	50666538	1.65e-05	160	2.07e-05	0.0399617	3
6	33280198	33280228	2.17e-05	30	2.17e-05	0.2481969	3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr/Cr_log2_manhattan_DMP_adj.png")

Cr, female

DMP_Cr_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26701 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  25525 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.205679 
 
# Number of identified DMR:  0

# rm(DMP_Cr_F); gc()

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F/Cr_log2_manhattan_DMP_adj.png")

Cr, male

DMP_Cr_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  17887 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12255 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8668368 
 
# Number of DMRs identified:   1 

# rm(DMP_Cr_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	46685291	46685448	0	157	0	3.4e-06	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M/Cr_log2_manhattan_DMP_adj.png")

Cs

DMP_Cs = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  16687 
# Unadjusted, FDR<0.05:  4 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  13041 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8278941 
 
# Number of DMRs identified:   6 

# rm(DMP_Cs); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	32847584	32847845	0.0000000	261	0.0000000	0.0000152	14
6	33280051	33280228	0.0000000	177	0.0000000	0.0000334	6
13	47472049	47472429	0.0000000	380	0.0000001	0.0000285	12
10	94820922	94821085	0.0000001	163	0.0000001	0.0002097	6
1	68512776	68512928	0.0000636	152	0.0000763	0.1521621	4
20	57427641	57427762	0.0010790	121	0.0010790	0.9703825	6

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs/Cs_log2_manhattan_DMP_adj.png")

Cs, female

DMP_Cs_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  25871 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16221 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9629794 
 
# Number of DMRs identified:   3 

# rm(DMP_Cs_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
1	200272111	200272215	0	104	0	7.60e-06	3
20	3145355	3145597	0	242	0	1.60e-05	3
6	29648378	29648628	0	250	0	1.97e-05	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F/Cs_log2_manhattan_DMP_adj.png")

Cs, male

DMP_Cs_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15896 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13428 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.853948 
 
# Number of DMRs identified:   2 
 
# rm(DMP_Cs_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	57427442	57427942	0.0000000	500	0.0000000	0.0000005	16
1	68512776	68512845	0.0026516	69	0.0026516	0.9999997	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M/Cs_log2_manhattan_DMP_adj.png")

Cu

DMP_Cu = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  10199 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19996 
# Adjusted, FDR<0.05:  29 
# Adjusted, pBonf<0.05:  9 
# Adjusted, lambda:  1.081714 
 
# Number of DMRs identified:   18 

# rm(DMP_Cu); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
1551	cg00082497	-0.2520409	-0.3556952	-0.1483866	-5.3168403	-4.784067	2.6e-06	0.0359038	2.498822	1.0000000	0.0525407	chr1	32802133	MARCKSL1	32802133
2216	cg00116766	0.4187686	0.2817760	0.5557613	2.0369340	6.014386	0.0e+00	0.0013375	6.661993	0.0019672	0.0696696	chr16	9857614	GRIN2A;GRIN2A;GRIN2A	9857614
15593	cg00908120	0.5161498	0.3285615	0.7037382	6.2592960	5.413594	1.0e-07	0.0053672	4.536415	0.0483052	0.0955715	chr16	72872925	ZFHX3;ZFHX3	72872925
36122	cg02155957	0.3783738	0.2317081	0.5250394	3.2458879	5.075841	7.0e-07	0.0144647	3.418015	0.2603651	0.0746248	chr1	46930731		46930731
66105	cg04015129	0.6991493	0.4380113	0.9602872	4.2830360	5.267633	3.0e-07	0.0077753	4.046096	0.1010794	0.1331776	chr10	1058036	GTPBP4	1058036
76780	cg04692924	-0.4221533	-0.5884130	-0.2558937	-6.6080183	-4.995731	1.0e-06	0.0182608	3.161088	0.3834770	0.0846568	chr1	161720042	DUSP12	161720042
82479	cg05051957	-0.4539930	-0.6266037	-0.2813824	-5.5960973	-5.174845	4.0e-07	0.0103119	3.739885	0.1603134	0.0879075	chr8	141522459	CHRAC1;CHRAC1	141522459
96056	cg05955013	-0.3954311	-0.5455648	-0.2452975	-6.2800794	-5.182132	4.0e-07	0.0103119	3.763782	0.1546451	0.0763997	chr17	45056646	RPRML	45056646
107200	cg06723863	-0.2584074	-0.3627173	-0.1540976	-5.9821329	-4.874088	1.7e-06	0.0262890	2.777821	0.6835148	0.0528782	chr16	68270129	ESRP2;ESRP2	68270129
117957	cg07380021	-0.5074974	-0.6911466	-0.3238481	-5.4168894	-5.437012	1.0e-07	0.0053558	4.616053	0.0428465	0.0935562	chr1	206755252	RASSF5;RASSF5;RASSF5	206755252
124637	cg07831553	0.6064739	0.3579392	0.8550087	3.3703905	4.801100	2.4e-06	0.0343734	2.550888	0.9624563	0.1267359	chr19	48796974		48796974
132730	cg08370347	0.5104082	0.3050049	0.7158114	3.9077562	4.889066	1.6e-06	0.0254900	2.824231	0.6372491	0.1046840	chr5	171571793	STK10	171571793
157990	cg10145926	0.6116469	0.3869329	0.8363609	5.3066802	5.355331	2.0e-07	0.0059077	4.339440	0.0649842	0.1145586	chr14	95875792	C14orf139	95875792
165306	cg10653573	0.8216430	0.4935682	1.1497177	5.4323036	4.927492	1.3e-06	0.0241467	2.944904	0.5312281	0.1673806	chr8	141347297	TRAPPC9;TRAPPC9	141347297
168880	cg10923018	0.2400925	0.1567575	0.3234276	2.7547510	5.668452	0.0e+00	0.0025621	5.418042	0.0128106	0.0420591	chr6	31743769	C6orf27	31743769
178008	cg11608893	0.6111347	0.3655771	0.8566923	6.0473017	4.896652	1.6e-06	0.0254900	2.847992	0.6148187	0.1252142	chr6	32059542	TNXB	32059542
184513	cg12067421	-0.4638647	-0.6195019	-0.3082274	2.0086375	-5.863991	0.0e+00	0.0014972	6.113861	0.0044916	0.0792183	chr1	203246482		203246482
202444	cg13434714	-0.4198573	-0.5838480	-0.2558666	-5.7702697	-5.037302	8.0e-07	0.0165199	3.293966	0.3138780	0.0834953	chr12	6936787	LEPREL2	6936787
238372	cg15790767	1.0460317	0.6730623	1.4190011	3.8395189	5.518071	1.0e-07	0.0040292	4.893762	0.0282044	0.1903147	chr6	13431216	GFOD1	13431216
257054	cg17143270	0.8262133	0.5117283	1.1406983	5.7439128	5.169016	4.0e-07	0.0103119	3.720792	0.1649911	0.1604376	chr1	91532819		91532819
272331	cg18299835	-0.2325838	-0.3271320	-0.1380356	-4.1342108	-4.839937	2.0e-06	0.0297198	2.671477	0.8024340	0.0478488	chr19	13207445	NFIX	13207445
277756	cg18714712	-0.5396013	-0.7177693	-0.3614334	-5.9732941	-5.958802	0.0e+00	0.0013375	6.457915	0.0026750	0.0907515	chr19	49866917	DKKL1;TEAD2	49866917
288096	cg19532212	0.4901147	0.3073681	0.6728612	4.4622674	5.276722	2.0e-07	0.0077753	4.076321	0.0965815	0.0930943	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C	56769430
292461	cg19842134	-0.2877291	-0.4005045	-0.1749537	-3.5252232	-5.019759	9.0e-07	0.0170704	3.238255	0.3414082	0.0572337	chr12	54070591	ATP5G2;ATP5G2	54070591
299106	cg20365618	-0.2427541	-0.3400297	-0.1454786	0.4203879	-4.909944	1.5e-06	0.0250879	2.890132	0.5770213	0.0492549	chr10	121578384	INPP5F;INPP5F	121578384
338217	cg23477849	0.2847709	0.1875717	0.3819701	4.8779575	5.764299	0.0e+00	0.0019215	5.757320	0.0076859	0.0492155	chr19	5698492	LONP1	5698492
370410	cg25954729	-0.2214209	-0.3023661	-0.1404758	-6.3449744	-5.381973	1.0e-07	0.0056715	4.429925	0.0567155	0.0408229	chr11	66610784	RCE1;C11orf80;RCE1	66610784
381104	cg26708724	0.6610798	0.4075131	0.9146465	6.7325633	5.129526	5.0e-07	0.0117853	3.591901	0.2003502	0.1293079	chr4	187509785	FAT1	187509785
393045	cg27565067	0.4808885	0.3122348	0.6495422	6.2036309	5.610017	0.0e+00	0.0029086	5.212584	0.0174516	0.0858822	chr17	149484	RPH3AL	149484

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
22	45704901	45705265	0.0e+00	364	0.0e+00	0.0000000	7
20	35169538	35169886	0.0e+00	348	0.0e+00	0.0000000	6
16	66304366	66304585	0.0e+00	219	0.0e+00	0.0000001	3
10	121578136	121578639	0.0e+00	503	0.0e+00	0.0000001	4
12	54070516	54070610	0.0e+00	94	0.0e+00	0.0000006	5
16	8806530	8806756	0.0e+00	226	0.0e+00	0.0000005	7
17	149483	149488	0.0e+00	5	0.0e+00	0.0001478	2
6	1604012	1604212	0.0e+00	200	0.0e+00	0.0000156	5
20	3052114	3052483	0.0e+00	369	0.0e+00	0.0000175	9
17	1395863	1396123	0.0e+00	260	0.0e+00	0.0000380	5
19	55660590	55660625	0.0e+00	35	0.0e+00	0.0002927	4
15	100048370	100048500	0.0e+00	130	0.0e+00	0.0000987	3
2	130345204	130345405	0.0e+00	201	1.0e-07	0.0000951	3
17	47091977	47092178	1.0e-07	201	1.0e-07	0.0001346	4
19	50194119	50194252	1.0e-07	133	1.0e-07	0.0002220	5
13	100310161	100310405	1.0e-07	244	1.0e-07	0.0001692	4
11	19736149	19736333	1.0e-07	184	1.0e-07	0.0002958	5
1	207082827	207082900	1.1e-06	73	1.1e-06	0.0057588	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu/Cu_log2_manhattan_DMP_adj.png")

Cu, female

DMP_Cu_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  19233 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16206 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9568499 
 
# Number of DMRs identified:   11 

# rm(DMP_Cu_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
5	191295	191806	0.0000000	511	0.0000000	0.0000000	9
6	32063990	32064810	0.0000000	820	0.0000000	0.0000000	30
15	81426346	81426610	0.0000000	264	0.0000000	0.0000002	7
11	73357094	73357396	0.0000000	302	0.0000001	0.0000436	7
2	74875226	74875536	0.0000001	310	0.0000001	0.0000721	7
1	120174148	120174361	0.0000001	213	0.0000002	0.0002162	2
17	1395863	1396123	0.0000001	260	0.0000002	0.0002000	5
21	37442288	37442476	0.0000001	188	0.0000002	0.0002909	3
8	95962351	95962383	0.0000021	32	0.0000025	0.0252792	4
19	23941312	23941438	0.0001150	126	0.0001265	0.3023269	3
6	31734291	31734401	0.0008058	110	0.0008058	0.9444595	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F/Cu_log2_manhattan_DMP_adj.png")

Cu, male

DMP_Cu_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  8255 
# Unadjusted, FDR<0.05:  32 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  11955 
# Adjusted, FDR<0.05:  43 
# Adjusted, pBonf<0.05:  13 
# Adjusted, lambda:  0.732688 
 
# Number of DMRs identified:   13 

# rm(DMP_Cu_M); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
15593	cg00908120	0.6968301	0.4462335	0.9474266	6.2892750	5.491907	2.0e-07	0.0043618	3.025092	0.0610657	0.1275144	chr16	72872925	ZFHX3;ZFHX3	72872925
17338	cg01007589	0.9199500	0.5976038	1.2422962	4.7896683	5.636547	1.0e-07	0.0027740	3.404180	0.0305142	0.1642702	chr19	49894178	CCDC155	49894178
18335	cg01063965	-0.2697333	-0.3700510	-0.1694156	-6.4353826	-5.310319	4.0e-07	0.0095478	2.558610	0.1432177	0.0499143	chr11	695461	TMEM80;TMEM80;DEAF1;DEAF1	695461
24635	cg01447660	0.3857890	0.2320438	0.5395341	-0.9207246	4.955781	1.8e-06	0.0211997	1.670256	0.7207908	0.0777249	chr2	69152678		69152678
25210	cg01485439	0.5040485	0.3119450	0.6961521	3.6452587	5.182127	7.0e-07	0.0123633	2.231633	0.2596284	0.0974910	chr11	67225937	CABP4	67225937
36122	cg02155957	0.4849601	0.2932852	0.6766350	3.2214886	4.997028	1.5e-06	0.0198854	1.770337	0.6006643	0.0972710	chr1	46930731		46930731
41497	cg02490920	0.3674539	0.2288810	0.5060267	1.3358885	5.237070	5.0e-07	0.0105880	2.372126	0.2011721	0.0698665	chr3	50304406	SEMA3B;SEMA3B	50304406
49479	cg02968175	0.3051401	0.1909359	0.4193442	5.7555141	5.276926	4.0e-07	0.0098398	2.473410	0.1672768	0.0571880	chr16	4690020	MGRN1;MGRN1;MGRN1;MGRN1	4690020
61452	cg03717239	0.2988200	0.1782864	0.4193536	0.5057733	4.896268	2.4e-06	0.0247759	1.524790	0.9385842	0.0604897	chr8	145574318		145574318
66105	cg04015129	0.8389384	0.5547224	1.1231543	4.2710633	5.829792	0.0e+00	0.0013191	3.918551	0.0118723	0.1447437	chr10	1058036	GTPBP4	1058036
72385	cg04406071	-0.2980754	-0.4100451	-0.1861057	-6.0707229	-5.257620	5.0e-07	0.0101631	2.424293	0.1829363	0.0560206	chr17	59489784	C17orf82	59489784
76780	cg04692924	-0.5914287	-0.8226470	-0.3602104	-6.5844679	-5.051864	1.2e-06	0.0187815	1.905864	0.4695367	0.1175757	chr1	161720042	DUSP12	161720042
82479	cg05051957	-0.6067193	-0.8484554	-0.3649831	-5.6069817	-4.956986	1.8e-06	0.0211997	1.671792	0.7183584	0.1229709	chr8	141522459	CHRAC1;CHRAC1	141522459
96056	cg05955013	-0.4736694	-0.6647461	-0.2825927	-6.2968923	-4.895966	2.4e-06	0.0247759	1.522807	0.9414854	0.0969641	chr17	45056646	RPRML	45056646
117957	cg07380021	-0.6727208	-0.8917216	-0.4537201	-5.4253082	-6.066814	0.0e+00	0.0010386	4.560897	0.0036354	0.1113060	chr1	206755252	RASSF5;RASSF5;RASSF5	206755252
132177	cg08329655	-0.4301609	-0.5996488	-0.2606731	-5.8759956	-5.012548	1.4e-06	0.0198854	1.809564	0.5595710	0.0858576	chr11	7534677	PPFIBP2	7534677
133940	cg08459368	0.5800924	0.3505524	0.8096324	2.7047867	4.991261	1.6e-06	0.0198854	1.756039	0.6164462	0.1167147	chr11	61974948	SCGB2A1	61974948
138326	cg08760128	0.3023438	0.1838403	0.4208473	6.7313293	5.038874	1.3e-06	0.0191075	1.875166	0.4967943	0.0594315	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1	4723507
159790	cg10266648	1.0455372	0.6777917	1.4132828	5.9758418	5.615177	1.0e-07	0.0028193	3.347846	0.0338314	0.1875055	chr2	106560529		106560529
168880	cg10923018	0.3493522	0.2386925	0.4600120	2.7253233	6.235017	0.0e+00	0.0007687	5.027037	0.0015374	0.0553357	chr6	31743769	C6orf27	31743769
178008	cg11608893	0.9384948	0.6293671	1.2476226	6.0805801	5.996051	0.0e+00	0.0010386	4.367865	0.0051911	0.1575025	chr6	32059542	TNXB	32059542
202444	cg13434714	-0.6677598	-0.8632470	-0.4722727	-5.7834106	-6.746422	0.0e+00	0.0001057	6.462646	0.0001057	0.0992288	chr12	6936787	LEPREL2	6936787
211983	cg13989834	0.5445790	0.3327048	0.7564532	3.1425732	5.076382	1.1e-06	0.0175131	1.966788	0.4203137	0.1076471	chr9	134400392	UCK1;UCK1	134400392
232975	cg15389183	-0.2174854	-0.3060013	-0.1289694	-6.1941560	-4.852574	2.9e-06	0.0291746	1.418688	1.0000000	0.0436880	chr14	102829482	TECPR2;CINP	102829482
238372	cg15790767	1.1582593	0.6788697	1.6376489	3.8648959	4.771870	4.1e-06	0.0386055	1.223075	1.0000000	0.2446072	chr6	13431216	GFOD1	13431216
242146	cg16068812	-1.0140695	-1.4211959	-0.6069431	-4.2669662	-4.919374	2.2e-06	0.0241887	1.579759	0.8489923	0.2076521	chr21	44528396	U2AF1;U2AF1;U2AF1	44528396
248112	cg16496814	0.2786227	0.1688097	0.3884356	5.2206210	5.011024	1.4e-06	0.0198854	1.806255	0.5630518	0.0548928	chr11	9778721		9778721
250632	cg16656826	0.3287551	0.2038843	0.4536259	0.1436170	5.199664	6.0e-07	0.0119506	2.277470	0.2390116	0.0627483	chr5	159343871	ADRA1B;ADRA1B	159343871
277216	cg18670846	0.7273051	0.4270507	1.0275594	-2.3046149	4.784083	3.9e-06	0.0382303	1.252345	1.0000000	0.1529585	chr2	68917482		68917482
277756	cg18714712	-0.7278273	-0.9713903	-0.4842644	-5.9498636	-5.901856	0.0e+00	0.0010386	4.112559	0.0083088	0.1239078	chr19	49866917	DKKL1;TEAD2	49866917
281545	cg19005275	0.6770397	0.4430316	0.9110478	4.2897154	5.714189	1.0e-07	0.0020931	3.609791	0.0209309	0.1190070	chr12	113588263	CCDC42B	113588263
288096	cg19532212	0.6853542	0.4290550	0.9416534	4.4209486	5.281281	4.0e-07	0.0098398	2.482710	0.1643357	0.1304380	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C	56769430
299106	cg20365618	-0.3482548	-0.4639507	-0.2325589	0.4046566	-5.944876	0.0e+00	0.0010386	4.231669	0.0066813	0.0579668	chr10	121578384	INPP5F;INPP5F	121578384
301945	cg20597842	0.9761061	0.5701079	1.3821044	5.8802068	4.748367	4.6e-06	0.0417512	1.166880	1.0000000	0.2070751	chr12	7818585	APOBEC1	7818585
311691	cg21373263	0.7831825	0.4817236	1.0846414	3.2926911	5.131051	8.0e-07	0.0149060	2.103265	0.3279323	0.1535754	chr10	126751982	CTBP2;CTBP2	126751982
317735	cg21864868	0.6556443	0.4008014	0.9104871	4.2151756	5.081211	1.0e-06	0.0175131	1.978806	0.4112293	0.1296914	chr17	46673002	LOC404266;LOC404266;LOC404266;LOC404266;LOC404266	46673002
322216	cg22240394	1.0541992	0.6343256	1.4740728	6.8239404	4.958788	1.8e-06	0.0211997	1.676215	0.7126127	0.2141721	chr3	186211630		186211630
322745	cg22286640	-0.7778819	-1.0993127	-0.4564511	-4.6467158	-4.779666	4.0e-06	0.0382303	1.241753	1.0000000	0.1638016	chr8	67026828		67026828
336099	cg23312431	0.3344962	0.2000374	0.4689549	-0.3693187	4.913215	2.2e-06	0.0241887	1.566102	0.8707948	0.0677317	chr21	45773997	TRPM2	45773997
338217	cg23477849	0.3799812	0.2454369	0.5145256	4.8962493	5.577768	1.0e-07	0.0031066	3.251684	0.0403856	0.0677761	chr19	5698492	LONP1	5698492
352329	cg24543538	0.8446393	0.5105801	1.1786986	3.2168166	4.993663	1.5e-06	0.0198854	1.761957	0.6098552	0.1702661	chr2	241569846	GPR35	241569846
370410	cg25954729	-0.3031186	-0.4042129	-0.2020244	-6.3724574	-5.921746	0.0e+00	0.0010386	4.169016	0.0074984	0.0503223	chr11	66610784	RCE1;C11orf80;RCE1	66610784
381104	cg26708724	0.9627258	0.6436003	1.2818513	6.7173655	5.958165	0.0e+00	0.0010386	4.264949	0.0062755	0.1626214	chr4	187509785	FAT1	187509785

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	121578136	121578846	0.0000000	710	0.0000000	0.0000000	5
22	45704901	45705265	0.0000000	364	0.0000000	0.0000000	7
21	45773781	45773997	0.0000000	216	0.0000000	0.0000015	2
4	24796918	24797176	0.0000000	258	0.0000000	0.0000032	6
19	50194119	50194252	0.0000000	133	0.0000000	0.0000267	5
17	70723226	70723386	0.0000000	160	0.0000000	0.0000317	2
20	35169593	35169886	0.0000000	293	0.0000001	0.0000422	5
14	78447480	78447640	0.0000001	160	0.0000001	0.0001307	3
3	16216093	16216215	0.0000001	122	0.0000001	0.0001905	4
17	78549323	78549371	0.0000001	48	0.0000001	0.0006222	3
17	149483	149488	0.0000001	5	0.0000001	0.0080723	2
12	54070516	54070591	0.0000149	75	0.0000161	0.0752227	4
16	8806752	8806756	0.0029944	4	0.0029944	1.0000000	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M/Cu_log2_manhattan_DMP_adj.png")

Hg

DMP_Hg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg')

# Unadjusted, N =  326 
# Unadjusted, p<0.05:  37293 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  326 
# Adjusted, p<0.05:  27145 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.2206 
 
# Number of DMRs identified:   4 

# rm(DMP_Hg); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	46681110	46681401	0.0000000	291	0.0000000	0.0000007	6
6	31846768	31847009	0.0000000	241	0.0000000	0.0000093	9
10	131843516	131843725	0.0000022	209	0.0000030	0.0042060	3
3	42977952	42978026	0.0004262	74	0.0004262	0.8969299	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg/Hg_log2_manhattan_DMP_adj.png")

Hg, female

DMP_Hg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F')

# Unadjusted, N =  154 
# Unadjusted, p<0.05:  35686 
# Unadjusted, FDR<0.05:  156 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  154 
# Adjusted, p<0.05:  15067 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8813254 
 
# Number of DMRs identified:   3 

# rm(DMP_Hg_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
12	47219625	47220092	0	467	0	0.00e+00	12
4	165877874	165878136	0	262	0	2.10e-06	6
7	27143234	27143478	0	244	0	2.93e-05	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F/Hg_log2_manhattan_DMP_adj.png")

Hg, male

DMP_Hg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M')

# Unadjusted, N =  172 
# Unadjusted, p<0.05:  22412 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  172 
# Adjusted, p<0.05:  24779 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.2248 
 
# Number of DMRs identified:   7 

# rm(DMP_Hg_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	31846768	31847009	0e+00	241	0e+00	0.0000000	9
11	18477152	18477534	0e+00	382	0e+00	0.0000001	7
11	18433499	18433887	0e+00	388	0e+00	0.0000001	5
5	502290	502571	0e+00	281	0e+00	0.0000015	3
6	33282735	33283162	0e+00	427	0e+00	0.0000011	20
14	104690039	104690244	0e+00	205	0e+00	0.0000132	5
1	2345151	2345410	1e-07	259	1e-07	0.0001903	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M/Hg_log2_manhattan_DMP_adj.png")

Mg

DMP_Mg = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  18232 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15989 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8804657 
 
# Number of DMRs identified:   4 

# rm(DMP_Mg); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	3051953	3052345	0.0e+00	392	0.0e+00	0.0000000	9
6	31543539	31543686	0.0e+00	147	0.0e+00	0.0000326	8
2	240196768	240196996	0.0e+00	228	1.0e-07	0.0000792	3
11	368564	368712	1.9e-06	148	1.9e-06	0.0049840	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg/Mg_log2_manhattan_DMP_adj.png")

Mg, female

DMP_Mg_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  33977 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  20666 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.081664 
 
# Number of DMRs identified:   2 

# rm(DMP_Mg_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
2	240196876	240196996	0.0000008	120	0.0000016	0.0025678	2
6	10884093	10884140	0.0002591	47	0.0002591	0.8863834	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F/Mg_log2_manhattan_DMP_adj.png")

Mg, male

DMP_Mg_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  9395 
# Unadjusted, FDR<0.05:  7 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13518 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8045591 

# Number of identified DMR:  0

# rm(DMP_Mg_M); gc()

FDR-significant DMPs

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
21	45773781	45773997	0.0000000	216	0.0000000	0.0000013	2
17	37123637	37123949	0.0000000	312	0.0000001	0.0000317	9
5	23507449	23507656	0.0000000	207	0.0000002	0.0000915	5
2	152830504	152830665	0.0000001	161	0.0000003	0.0002264	5
17	47091977	47092178	0.0000001	201	0.0000003	0.0002324	4
10	121578383	121578639	0.0000003	256	0.0000005	0.0003992	3
6	31543539	31543686	0.0000004	147	0.0000006	0.0010323	8
3	138725152	138725425	0.0000004	273	0.0000006	0.0006235	7
12	54385274	54385526	0.0000008	252	0.0000009	0.0012112	4
17	70723226	70723386	0.0000013	160	0.0000014	0.0032358	2
11	368564	368638	0.0002279	74	0.0002279	0.7033206	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M/Mg_log2_manhattan_DMP_adj.png")

Mn

DMP_Mn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  27983 
# Unadjusted, FDR<0.05:  6 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  39149 
# Adjusted, FDR<0.05:  14 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.35996 
 
# Number of DMRs identified:   7 

# rm(DMP_Mn); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
13985	cg00808511	0.1797749	0.1076657	0.2518840	2.8599969	4.905172	1.5e-06	0.0441677	4.921202	0.5905329	0.0367425	chr16	52495237	TOX3;TOX3	52495237
61437	cg03716590	0.1820431	0.1108155	0.2532707	5.0904967	5.028534	8.0e-07	0.0327455	5.457274	0.3274551	0.0362916	chr7	95435309	DYNC1I1;DYNC1I1;DYNC1I1	95435309
90890	cg05613017	0.1995162	0.1227136	0.2763187	5.3286885	5.111142	6.0e-07	0.0272713	5.822518	0.2192172	0.0391431	chr12	65589446	LEMD3;LEMD3	65589446
153815	cg09856068	-0.1132155	-0.1568602	-0.0695708	-4.3655995	-5.103735	6.0e-07	0.0272713	5.790109	0.2271515	0.0221605	chr5	170878246	FGF18	170878246
170758	cg11063328	-0.1609044	-0.2222669	-0.0995418	-6.0173655	-5.159174	4.0e-07	0.0272713	6.037176	0.1731901	0.0312433	chr11	18343203	GTF2H1;HPS5;HPS5;HPS5;GTF2H1	18343203
171438	cg11115211	-0.1889357	-0.2648699	-0.1130014	-5.8811483	-4.895440	1.6e-06	0.0441677	4.879395	0.6183473	0.0386990	chr3	67704890	SUCLG2	67704890
209344	cg13834844	-0.1019035	-0.1391228	-0.0646842	-5.1364932	-5.386845	1.0e-07	0.0138315	7.077995	0.0553259	0.0188544	chr10	102415320		102415320
216559	cg14252211	0.1929530	0.1274370	0.2584689	5.8503162	5.794555	0.0e+00	0.0032695	9.031255	0.0065390	0.0333691	chr1	25919394		25919394
286458	cg19407717	0.3110043	0.2209750	0.4010336	4.0277865	6.796700	0.0e+00	0.0000211	14.301558	0.0000211	0.0459058	chr2	1544120	TPO;TPO;TPO;TPO	1544120
286677	cg19425870	-0.1477253	-0.2059407	-0.0895098	-6.4570149	-4.992663	1.0e-06	0.0353787	5.300234	0.3891653	0.0296320	chr11	3876808	STIM1	3876808
326256	cg22586726	0.2701506	0.1619704	0.3783308	-0.9735686	4.913305	1.4e-06	0.0441677	4.956198	0.5682174	0.0551823	chr10	134150542	LRRC27;LRRC27;LRRC27;LRRC27;LRRC27	134150542
347861	cg24196240	0.3273967	0.2094577	0.4453357	5.2479144	5.461758	1.0e-07	0.0125768	7.427654	0.0377305	0.0601685	chr21	36096009	NCRNA00160	36096009
359777	cg25101184	0.2474977	0.1517913	0.3432040	3.3810389	5.087987	6.0e-07	0.0272713	5.719635	0.2454421	0.0488076	chr14	56231604	RPL13AP3	56231604
386595	cg27095984	-0.1889690	-0.2595782	-0.1183597	5.2710750	-5.265561	3.0e-07	0.0204265	6.518590	0.1021325	0.0359752	chr13	21652115		21652115

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	134150488	134150760	0.0000000	272	0.0000000	0.0000000	7
19	21657528	21657756	0.0000000	228	0.0000000	0.0000001	4
16	30572738	30573013	0.0000000	275	0.0000000	0.0000011	5
16	73100425	73100510	0.0000000	85	0.0000000	0.0001111	2
10	45406680	45406847	0.0000000	167	0.0000000	0.0000744	3
20	61659979	61660250	0.0000001	271	0.0000001	0.0000929	2
10	35484767	35484824	0.0002039	57	0.0002039	0.7560663	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn/Mn_log2_manhattan_DMP_adj.png")

Mn, female

DMP_Mn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  28256 
# Unadjusted, FDR<0.05:  3 
# Unadjusted, pBonf<0.05:  3 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  40111 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.365691 
 
# Number of DMRs identified:   2 

# rm(DMP_Mn_F); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
170758	cg11063328	-0.2542536	-0.3311487	-0.1773585	-6.003312	-6.536372	0e+00	0.0004165	11.101209	0.0004165	0.0390272	chr11	18343203	GTF2H1;HPS5;HPS5;HPS5;GTF2H1	18343203
286677	cg19425870	-0.2408160	-0.3166778	-0.1649541	-6.446281	-6.275239	0e+00	0.0007852	9.941850	0.0015705	0.0384954	chr11	3876808	STIM1	3876808
324070	cg22396353	-0.1482285	-0.2007424	-0.0957146	-6.101068	-5.579761	1e-07	0.0154847	6.983409	0.0464542	0.0264223	chr22	46692687	GTSE1;GTSE1;CN5H6.4	46692687

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	3849380	3849702	0.0e+00	322	1.0e-07	0.0000351	13
11	76839190	76839217	5.3e-06	27	5.3e-06	0.0742406	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F/Mn_log2_manhattan_DMP_adj.png")

Mn, male

DMP_Mn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M')

Unadjusted, N =  175 
Unadjusted, p<0.05:  14905 
Unadjusted, FDR<0.05:  27 
Unadjusted, pBonf<0.05:  9 
 
Adjusted, N =  175 
Adjusted, p<0.05:  19138 
Adjusted, FDR<0.05:  30 
Adjusted, pBonf<0.05:  13 
Adjusted, lambda:  0.9881206 
 
Number of DMRs identified:   12 

# rm(DMP_Mn_M); gc()

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M/Mn_log2_manhattan_DMP_adj.png")

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
56695	cg03425412	-0.2215880	-0.3084393	-0.1347367	-5.940582	-5.038959	1.3e-06	0.0226177	4.630103	0.4975885	0.0440754	chr20	21500337		21500337
68153	cg04143120	0.4096425	0.2732188	0.5460663	6.792018	5.930435	0.0e+00	0.0010296	8.159475	0.0072071	0.0694995	chr11	72968848		72968848
79809	cg04885068	0.1877474	0.1216510	0.2538439	6.474553	5.609957	1.0e-07	0.0032325	6.851750	0.0345882	0.0333719	chr1	9099298	SLC2A5;SLC2A5	9099298
82300	cg05041382	-0.1229809	-0.1725540	-0.0734078	-6.391825	-4.899538	2.3e-06	0.0330400	4.114159	0.9251202	0.0247765	chr13	50366546	KPNA3	50366546
85445	cg05249026	-0.1644832	-0.2257280	-0.1032385	-2.355604	-5.304156	4.0e-07	0.0081883	5.643430	0.1473888	0.0308565	chr16	11031524	DEXI	11031524
97510	cg06051716	0.3566344	0.2441486	0.4691202	6.493667	6.261770	0.0e+00	0.0002468	9.558316	0.0013459	0.0572337	chr6	169225783		169225783
107728	cg06756211	-0.2081794	-0.2740447	-0.1423141	-6.049441	-6.242302	0.0e+00	0.0002468	9.478836	0.0014809	0.0332522	chr1	223936799	CAPN2;CAPN2	223936799
109948	cg06883949	-0.1214334	-0.1679112	-0.0749557	-6.468868	-5.160082	7.0e-07	0.0143290	5.089503	0.2865793	0.0231544	chr4	1795240	FGFR3;FGFR3;FGFR3	1795240
128092	cg08072480	-0.1393237	-0.1948333	-0.0838141	-6.612619	-4.957019	1.8e-06	0.0298678	4.326339	0.7168284	0.0278749	chr11	65292666	SCYL1;SCYL1	65292666
157031	cg10088075	-0.1106800	-0.1561537	-0.0652063	-6.213891	-4.806981	3.5e-06	0.0463062	3.776162	1.0000000	0.0226270	chr16	30407103	ZNF48;ZNF48	30407103
176390	cg11480534	0.3975879	0.2442723	0.5509035	5.838834	5.121748	9.0e-07	0.0162915	4.941954	0.3421211	0.0781475	chr11	62255850	AHNAK	62255850
176843	cg11521780	-0.1371987	-0.1836223	-0.0907750	-5.767858	-5.836788	0.0e+00	0.0014287	7.775114	0.0114294	0.0231260	chr12	53693949	C12orf10	53693949
180100	cg11755803	0.4054795	0.2439920	0.5669669	5.790724	4.959083	1.8e-06	0.0298678	4.332328	0.7116767	0.0823297	chr12	129000542	TMEM132C	129000542
192975	cg12700904	-0.1026171	-0.1442559	-0.0609784	-5.936497	-4.867273	2.7e-06	0.0367795	3.995819	1.0000000	0.0206063	chr3	13590720	FBLN2;FBLN2	13590720
194538	cg12828656	-0.1505408	-0.1978614	-0.1032201	-0.497092	-6.283003	0.0e+00	0.0002468	9.653365	0.0012011	0.0235966	chr5	132577108	FSTL4	132577108
209344	cg13834844	-0.1537219	-0.2150872	-0.0923565	-5.125143	-4.947389	1.9e-06	0.0299292	4.290672	0.7482293	0.0309191	chr10	102415320		102415320
209541	cg13848566	-0.1657616	-0.2254232	-0.1061000	-6.364105	-5.487225	2.0e-07	0.0041510	6.361612	0.0622649	0.0300344	chr9	89561175	GAS1	89561175
214672	cg14149680	-0.2933548	-0.3823188	-0.2043908	-6.352664	-6.512538	0.0e+00	0.0001218	10.644399	0.0003654	0.0451606	chr11	2187632	TH;TH;TH	2187632
249118	cg16560774	-0.1674158	-0.2247905	-0.1100411	-6.459545	-5.762880	0.0e+00	0.0018270	7.471818	0.0164430	0.0288456	chr17	79373381	BAHCC1	79373381
286458	cg19407717	0.4941274	0.3507014	0.6375534	4.033610	6.804284	0.0e+00	0.0000420	11.935137	0.0000775	0.0730850	chr2	1544120	TPO;TPO;TPO;TPO	1544120
287817	cg19511862	-0.1036380	-0.1427175	-0.0645584	-6.258253	-5.237605	5.0e-07	0.0105619	5.386300	0.2006761	0.0192509	chr12	125478458	BRI3BP	125478458
289598	cg19641404	-0.1138848	-0.1597132	-0.0680564	-5.865794	-4.907886	2.3e-06	0.0330400	4.144868	0.8915828	0.0228134	chr2	232826272	DIS3L2	232826272
299702	cg20414082	0.2602966	0.1634793	0.3571138	3.200594	5.309910	4.0e-07	0.0081883	5.663610	0.1438533	0.0491946	chr1	203002593		203002593
300828	cg20504533	-0.2169473	-0.2800653	-0.1538293	-5.852235	-6.788360	0.0e+00	0.0000420	11.869177	0.0000839	0.0318283	chr17	15848253	ADORA2B;ADORA2B	15848253
326031	cg22563312	-0.1654587	-0.2241965	-0.1067209	-6.274307	-5.563337	1.0e-07	0.0033295	6.664767	0.0432836	0.0295544	chr5	179334739	TBC1D9B;TBC1D9B	179334739
327739	cg22702772	-0.1485121	-0.2011945	-0.0958296	-6.685949	-5.567491	1.0e-07	0.0033295	6.681390	0.0424292	0.0264012	chr3	48699012	CELSR3	48699012
347861	cg24196240	0.4158514	0.2668619	0.5648410	5.267386	5.512565	1.0e-07	0.0039531	6.459776	0.0553431	0.0759332	chr21	36096009	NCRNA00160	36096009
357841	cg24948962	-0.2158814	-0.2919582	-0.1398046	-5.437432	-5.604397	1.0e-07	0.0032325	6.828678	0.0355576	0.0385319	chr18	2906032	EMILIN2	2906032
360532	cg25152909	0.4300346	0.2746166	0.5854525	6.076684	5.464792	2.0e-07	0.0043413	6.270370	0.0694607	0.0792235	chr5	172566090	C5orf41	172566090
364427	cg25466588	-0.0942618	-0.1322555	-0.0562681	-5.901716	-4.899910	2.3e-06	0.0330400	4.115528	0.9235979	0.0186738	chr3	23958904	NKIRAS1;RPL15	23958904

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
1	161008461	161008977	0.00e+00	516	0.00e+00	0.0000000	8
19	21657528	21658001	0.00e+00	473	0.00e+00	0.0000000	5
19	10736005	10736117	0.00e+00	112	0.00e+00	0.0000053	5
20	5485244	5485511	0.00e+00	267	0.00e+00	0.0000034	6
4	79971176	79971432	0.00e+00	256	0.00e+00	0.0000077	4
20	35169593	35169886	0.00e+00	293	0.00e+00	0.0000076	5
1	9099280	9099462	1.00e-07	182	1.00e-07	0.0001413	3
6	26018002	26018185	1.00e-07	183	2.00e-07	0.0002188	6
3	39543966	39544192	2.90e-06	226	3.80e-06	0.0050183	2
15	91473090	91473365	6.10e-06	275	7.40e-06	0.0087499	4
19	12444612	12444741	9.80e-06	129	1.06e-05	0.0293841	5
6	37616597	37616686	8.58e-05	89	8.58e-05	0.3164878	2

Pb

DMP_Pb = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  13157 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19418 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.040491 
 
# Number of DMRs identified:   8 

# rm(DMP_Pb); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	135051021	135051581	0.0000000	560	0.0000000	0.0000000	11
22	45704901	45705265	0.0000000	364	0.0000000	0.0000000	7
22	19746155	19746368	0.0000000	213	0.0000000	0.0000309	3
3	130745441	130745685	0.0000000	244	0.0000001	0.0000426	10
7	155283139	155283424	0.0000001	285	0.0000001	0.0001025	3
14	104690039	104690244	0.0000001	205	0.0000001	0.0001464	5
6	2891972	2892152	0.0000001	180	0.0000001	0.0001715	5
1	68512776	68512845	0.0001164	69	0.0001164	0.4859412	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb/Pb_log2_manhattan_DMP_adj.png")

Pb, female

DMP_Pb_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  10571 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  12301 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7551375 
 
# Number of identified DMR:  0

# rm(DMP_Pb_F); gc()

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F/Pb_log2_manhattan_DMP_adj.png")

Pb, male

DMP_Pb_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  18362 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12960 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8922977 
 
# Number of DMRs identified:   5 

# rm(DMP_Pb_M); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	33084548	33084985	0.0000000	437	0.0000000	0.0000000	12
1	68512649	68513063	0.0000000	414	0.0000000	0.0000001	7
6	31148331	31148748	0.0000000	417	0.0000000	0.0000008	14
22	45704987	45705265	0.0000001	278	0.0000001	0.0000883	5
19	55973098	55973234	0.0002395	136	0.0002395	0.5007541	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M/Pb_log2_manhattan_DMP_adj.png")

Se

DMP_Se = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  17270 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20323 
# Adjusted, FDR<0.05:  4 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.973855 
 
# Number of DMRs identified:   3 

# rm(DMP_Se); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
138326	cg08760128	0.2026753	0.1259450	0.2794056	6.725058	5.196935	4e-07	0.0449466	4.356067	0.1436282	0.0387600	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1	4723507
157990	cg10145926	0.5456661	0.3464279	0.7449044	5.306680	5.388525	1e-07	0.0274488	5.040732	0.0548975	0.1015708	chr14	95875792	C14orf139	95875792
202444	cg13434714	-0.4219050	-0.5657148	-0.2780953	-5.770270	-5.772209	0e+00	0.0073738	6.470917	0.0073738	0.0732155	chr12	6936787	LEPREL2	6936787
381104	cg26708724	0.5887632	0.3639014	0.8136251	6.732563	5.151581	5e-07	0.0449466	4.196202	0.1797863	0.1146694	chr4	187509785	FAT1	187509785

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	47091977	47092178	0	201	0	3.70e-06	4
19	50194119	50194252	0	133	0	1.48e-05	5
6	49681177	49681391	0	214	0	2.69e-05	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se/Se_log2_manhattan_DMP_adj.png")

Se, female

DMP_Se_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26254 
# Unadjusted, FDR<0.05:  9 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16021 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9294051 
 
# Number of DMRs identified:   3 

# rm(DMP_Se_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	49681177	49681391	0	214	0	7.00e-07	7
10	38146245	38146671	0	426	0	5.00e-07	9
10	38299241	38299574	0	333	0	1.76e-05	9

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F/Se_log2_manhattan_DMP_adj.png")

Se, male

DMP_Se_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15593 
# Unadjusted, FDR<0.05:  42 
# Unadjusted, pBonf<0.05:  12 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14283 
# Adjusted, FDR<0.05:  28 
# Adjusted, pBonf<0.05:  7 
# Adjusted, lambda:  0.8126609 
 
# Number of DMRs identified:   3 

# rm(DMP_Se_M); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
15593	cg00908120	0.5923048	0.3575326	0.8270770	6.2892750	4.982761	1.6e-06	0.0400205	1.992248	0.6403278	0.1194751	chr16	72872925	ZFHX3;ZFHX3	72872925
17338	cg01007589	0.7711724	0.4682737	1.0740712	4.7896683	5.028349	1.3e-06	0.0363003	2.109738	0.5219828	0.1543716	chr19	49894178	CCDC155	49894178
26849	cg01588060	-0.2710911	-0.3758947	-0.1662874	-5.9018630	-5.108606	9.0e-07	0.0301990	2.319787	0.3623878	0.0524668	chr6	2245749	GMDS;GMDS	2245749
76780	cg04692924	-0.5882409	-0.7990174	-0.3774643	-6.5844679	-5.511938	1.0e-07	0.0077706	3.394618	0.0555090	0.1071685	chr1	161720042	DUSP12	161720042
82479	cg05051957	-0.6574367	-0.8740830	-0.4407904	-5.6069817	-5.993411	0.0e+00	0.0013886	4.736594	0.0052603	0.1101799	chr8	141522459	CHRAC1;CHRAC1	141522459
107200	cg06723863	-0.3421497	-0.4652900	-0.2190094	-5.9860381	-5.487563	2.0e-07	0.0077706	3.330366	0.0621651	0.0620145	chr16	68270129	ESRP2;ESRP2	68270129
121260	cg07599133	-0.3416695	-0.4778828	-0.2054563	-5.9551590	-4.953937	1.8e-06	0.0427492	1.919754	0.7267357	0.0687928	chr19	35068628	LOC643719	35068628
178008	cg11608893	0.8339746	0.5460968	1.1218524	6.0805801	5.721582	1.0e-07	0.0040380	3.971861	0.0201898	0.1466815	chr6	32059542	TNXB	32059542
186947	cg12243007	0.4392467	0.2665983	0.6118950	-0.7662192	5.024766	1.3e-06	0.0363003	2.100794	0.5302302	0.0875896	chr17	184018	RPH3AL	184018
195368	cg12897502	-0.8409766	-1.1581637	-0.5237896	6.1025868	-5.236485	5.0e-07	0.0183820	2.654338	0.2022023	0.1616851	chr8	67425316	C8orf46	67425316
202444	cg13434714	-0.6278713	-0.8074616	-0.4482811	-5.7834106	-6.904931	0.0e+00	0.0000225	7.412530	0.0000450	0.0911537	chr12	6936787	LEPREL2	6936787
250632	cg16656826	0.2945037	0.1786042	0.4104032	0.1436170	5.018486	1.4e-06	0.0363003	2.085783	0.5445052	0.0582509	chr5	159343871	ADRA1B;ADRA1B	159343871
273355	cg18377660	0.7105200	0.4530993	0.9679406	5.6482645	5.451354	2.0e-07	0.0082254	3.229974	0.0740287	0.1310822	chr1	57535755	DAB1	57535755
281545	cg19005275	0.5865429	0.3677768	0.8053089	4.2897154	5.295308	4.0e-07	0.0153969	2.810608	0.1539686	0.1112673	chr12	113588263	CCDC42B	113588263
311691	cg21373263	0.8225623	0.5510102	1.0941144	3.2926911	5.982561	0.0e+00	0.0013886	4.705737	0.0055543	0.1383211	chr10	126751982	CTBP2;CTBP2	126751982
359398	cg25067702	-0.6449717	-0.8730675	-0.4168760	-6.4012877	-5.584637	1.0e-07	0.0065319	3.593491	0.0391915	0.1160520	chr17	70723227	SLC39A11;SLC39A11	70723227
381104	cg26708724	1.0174549	0.7331142	1.3017956	6.7173655	7.067202	0.0e+00	0.0000186	7.903550	0.0000186	0.1448704	chr4	187509785	FAT1	187509785

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	70723226	70723386	0.0000000	160	0.0000000	0.0000001	2
4	24796918	24797176	0.0000000	258	0.0000000	0.0000212	6
10	121578383	121578639	0.0000001	256	0.0000001	0.0001182	3
6	30039141	30039175	0.0047996	34	0.0047996	1.0000000	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M/Se_log2_manhattan_DMP_adj.png")

Zn

DMP_Zn = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  12854 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23377 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.10425 

# Number of DMRs identified:   13 

# rm(DMP_Zn); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
1551	cg00082497	-0.2789683	-0.3788872	-0.1790494	-5.316840	-5.493142	1.0e-07	0.0116179	5.179846	0.0320645	0.0506389	chr1	32802133	MARCKSL1	32802133
15593	cg00908120	0.4887949	0.3055657	0.6720241	6.259296	5.248649	3.0e-07	0.0171923	4.318434	0.1111402	0.0933516	chr16	72872925	ZFHX3;ZFHX3	72872925
66105	cg04015129	0.6544048	0.3991261	0.9096834	4.283036	5.043681	8.0e-07	0.0293642	3.620884	0.3043451	0.1301901	chr10	1058036	GTPBP4	1058036
90290	cg05573434	0.4125276	0.2574161	0.5676391	-3.154237	5.232686	3.0e-07	0.0171923	4.263312	0.1203459	0.0789613	chr4	7648540	SORCS2	7648540
107200	cg06723863	-0.2528131	-0.3544065	-0.1512197	-5.982133	-4.896069	1.6e-06	0.0473985	3.132897	0.6161801	0.0515011	chr16	68270129	ESRP2;ESRP2	68270129
133940	cg08459368	0.5943151	0.3801796	0.8084505	2.645733	5.460643	1.0e-07	0.0116179	5.062990	0.0379479	0.1091583	chr11	61974948	SCGB2A1	61974948
165306	cg10653573	0.8207249	0.5017201	1.1397297	5.432304	5.061929	7.0e-07	0.0293642	3.682080	0.2785931	0.1627524	chr8	141347297	TRAPPC9;TRAPPC9	141347297
202444	cg13434714	-0.4872777	-0.6443364	-0.3302191	-5.770270	-6.104221	0.0e+00	0.0011936	7.460402	0.0011936	0.0799582	chr12	6936787	LEPREL2	6936787
234745	cg15528091	-0.3070787	-0.4271830	-0.1869744	-6.355947	-5.030429	8.0e-07	0.0293642	3.577005	0.3242929	0.0610193	chr19	18119069	ARRDC2;ARRDC2;ARRDC2	18119069
248112	cg16496814	0.2140204	0.1314881	0.2965527	5.206564	5.102050	6.0e-07	0.0286288	3.817765	0.2290303	0.0416708	chr11	9778721		9778721
281636	cg19011752	0.2463497	0.1496666	0.3430328	-2.537801	5.013200	9.0e-07	0.0293642	3.519541	0.3523705	0.0489723	chr21	45772638	TRPM2	45772638
338217	cg23477849	0.2605321	0.1652481	0.3558161	4.877957	5.379658	1.0e-07	0.0116179	4.776453	0.0573879	0.0482514	chr19	5698492	LONP1	5698492
370410	cg25954729	-0.2155491	-0.2944166	-0.1366816	-6.344974	-5.377269	1.0e-07	0.0116179	4.768033	0.0580895	0.0397755	chr11	66610784	RCE1;C11orf80;RCE1	66610784

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
12	54070516	54070610	0.0000000	94	0.0000000	0.0000052	5
19	18118799	18119069	0.0000000	270	0.0000000	0.0000098	3
10	124638975	124639260	0.0000000	285	0.0000001	0.0000233	12
20	25129295	25129562	0.0000001	267	0.0000002	0.0001003	8
6	32063990	32064258	0.0000001	268	0.0000002	0.0001031	12
4	7648539	7648627	0.0000001	88	0.0000002	0.0003372	2
8	41655672	41655894	0.0000001	222	0.0000002	0.0002389	4
6	41168800	41169049	0.0000001	249	0.0000002	0.0002207	6
17	1395863	1396123	0.0000002	260	0.0000002	0.0002547	5
17	79503641	79503877	0.0000002	236	0.0000002	0.0002943	4
12	54385274	54385526	0.0000002	252	0.0000002	0.0002909	4
22	45704987	45705042	0.0000002	55	0.0000002	0.0014895	4
20	35169593	35169846	0.0004351	253	0.0004351	0.4926596	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn/Zn_log2_manhattan_DMP_adj.png")

Zn, female

DMP_Zn_F = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F')

# # Unadjusted, N =  158 
# Unadjusted, p<0.05:  12830 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  17143 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9412223 
 
# Number of DMRs identified:   3 

# rm(DMP_Zn_F); gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
11	73357018	73357396	0.0e+00	378	0.0e+00	0.0000000	8
1	120174148	120174361	7.0e-07	213	1.1e-06	0.0013294	2
10	124638975	124639012	1.1e-05	37	1.1e-05	0.1109657	4

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F/Zn_log2_manhattan_DMP_adj.png")

Zn, male

DMP_Zn_M = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16787 
# Unadjusted, FDR<0.05:  36 
# Unadjusted, pBonf<0.05:  8 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14737 
# Adjusted, FDR<0.05:  36 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8766913 
 
# Number of DMRs identified:   16 

# rm(DMP_Zn_M); gc()

FDR-significant DMPs

	cpg	logFC	CI.L	CI.R	AveExpr	t	P.Value	adj.P.Val	B	adj.P.Val.bonf	std_err	chr	pos	gene	end
15593	cg00908120	0.7986746	0.5264258	1.0709234	6.2892750	5.793958	0.0e+00	0.0052948	3.3135597	0.0141641	0.1385227	chr16	72872925	ZFHX3;ZFHX3	72872925
17338	cg01007589	0.9065622	0.5465007	1.2666237	4.7896683	4.972701	1.7e-06	0.0267901	1.3379386	0.6697528	0.1835056	chr19	49894178	CCDC155	49894178
18335	cg01063965	-0.2692683	-0.3808800	-0.1576566	-6.4353826	-4.764741	4.2e-06	0.0451214	0.8668535	1.0000000	0.0555811	chr11	695461	TMEM80;TMEM80;DEAF1;DEAF1	695461
24635	cg01447660	0.4161258	0.2471860	0.5850656	-0.9207246	4.864703	2.7e-06	0.0334209	1.0923878	1.0000000	0.0854122	chr2	69152678		69152678
25935	cg01533258	-0.3013596	-0.4269158	-0.1758034	-6.4562972	-4.740350	4.7e-06	0.0463873	0.8122693	1.0000000	0.0628818	chr14	95235489	GSC	95235489
36678	cg02196294	-0.2906897	-0.4099158	-0.1714636	-5.4126781	-4.815283	3.4e-06	0.0372147	0.9805256	1.0000000	0.0595727	chr6	39197260	KCNK5	39197260
41497	cg02490920	0.3948042	0.2423949	0.5472136	1.3358885	5.116039	9.0e-07	0.0166832	1.6720694	0.3503468	0.0768511	chr3	50304406	SEMA3B;SEMA3B	50304406
45187	cg02711608	0.5447487	0.3462840	0.7432134	-2.0855657	5.421025	2.0e-07	0.0122834	2.3968616	0.0853542	0.1006441	chr19	47287964	SLC1A5;SLC1A5;SLC1A5;SLC1A5	47287964
49479	cg02968175	0.3308394	0.2054185	0.4562602	5.7555141	5.209681	6.0e-07	0.0127085	1.8924369	0.2282507	0.0628111	chr16	4690020	MGRN1;MGRN1;MGRN1;MGRN1	4690020
55565	cg03352332	0.8979978	0.5628181	1.2331775	5.5379777	5.291381	4.0e-07	0.0123746	2.0848241	0.1568056	0.1707666	chr3	186360953	FETUB	186360953
66105	cg04015129	0.8663699	0.5510958	1.1816440	4.2710633	5.427334	2.0e-07	0.0122834	2.4113963	0.0829347	0.1605719	chr10	1058036	GTPBP4	1058036
71895	cg04374006	0.2627697	0.1559793	0.3695602	-0.2704598	4.859668	2.8e-06	0.0334209	1.0809686	1.0000000	0.0530461	chr19	33556395	RHPN2	33556395
72385	cg04406071	-0.3235390	-0.4464810	-0.2005970	-6.0707229	-5.197446	6.0e-07	0.0127085	1.8635148	0.2414621	0.0615161	chr17	59489784	C17orf82	59489784
76780	cg04692924	-0.6620566	-0.9146336	-0.4094796	-6.5844679	-5.176935	7.0e-07	0.0132956	1.8135106	0.2659111	0.1284330	chr1	161720042	DUSP12	161720042
82479	cg05051957	-0.6556186	-0.9211778	-0.3900594	-5.6069817	-4.875974	2.6e-06	0.0334209	1.1167256	1.0000000	0.1350923	chr8	141522459	CHRAC1;CHRAC1	141522459
107200	cg06723863	-0.3660155	-0.5147452	-0.2172859	-5.9860381	-4.860330	2.8e-06	0.0334209	1.0824690	1.0000000	0.0749420	chr16	68270129	ESRP2;ESRP2	68270129
117957	cg07380021	-0.6557600	-0.9015723	-0.4099477	-5.4253082	-5.268813	4.0e-07	0.0124371	2.0310571	0.1741199	0.1249619	chr1	206755252	RASSF5;RASSF5;RASSF5	206755252
138326	cg08760128	0.3591892	0.2311150	0.4872635	6.7313293	5.538922	1.0e-07	0.0121638	2.6848170	0.0486553	0.0641960	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1	4723507
143452	cg09127400	-0.3253080	-0.4612252	-0.1893909	-5.8091855	-4.726984	5.0e-06	0.0479454	0.7824329	1.0000000	0.0682830	chr6	30712331	IER3	30712331
159790	cg10266648	1.0393561	0.6292003	1.4495119	5.9758418	5.004802	1.5e-06	0.0241741	1.4119349	0.5801792	0.2091418	chr2	106560529		106560529
165306	cg10653573	1.4145550	0.8990686	1.9300414	5.3698793	5.419686	2.0e-07	0.0122834	2.3929054	0.0859836	0.2630143	chr8	141347297	TRAPPC9;TRAPPC9	141347297
168880	cg10923018	0.3112659	0.1850396	0.4374922	2.7253233	4.870183	2.7e-06	0.0334209	1.1048470	1.0000000	0.0632316	chr6	31743769	C6orf27	31743769
180170	cg11761483	-0.7173589	-0.9874920	-0.4472257	-5.5960630	-5.244814	5.0e-07	0.0127085	1.9740228	0.1945730	0.1374378	chr17	70723386	SLC39A11;SLC39A11	70723386
202444	cg13434714	-0.8386175	-1.0430621	-0.6341729	-5.7834106	-8.101361	0.0e+00	0.0000001	9.4776845	0.0000001	0.1037179	chr12	6936787	LEPREL2	6936787
216196	cg14230280	1.2229340	0.7320030	1.7138651	4.2784975	4.919874	2.1e-06	0.0313748	1.2167946	0.8471192	0.2504580	chr9	132502800	PTGES	132502800
248112	cg16496814	0.3215835	0.2022500	0.4409170	5.2206210	5.322247	3.0e-07	0.0123746	2.1603427	0.1354705	0.0596289	chr11	9778721		9778721
250632	cg16656826	0.3445219	0.2066488	0.4823949	0.1436170	4.935159	2.0e-06	0.0303861	1.2531114	0.7900373	0.0693009	chr5	159343871	ADRA1B;ADRA1B	159343871
257216	cg17155018	-1.0196926	-1.4432541	-0.5961312	1.3941337	-4.754713	4.4e-06	0.0455985	0.8432207	1.0000000	0.2160003	chr6	111953066		111953066
268589	cg18037826	0.4119927	0.2555297	0.5684556	4.2937576	5.200460	6.0e-07	0.0127085	1.8706351	0.2381405	0.0789525	chr12	109273835	DAO	109273835
281545	cg19005275	0.7482069	0.4921296	1.0042842	4.2897154	5.770615	0.0e+00	0.0052948	3.2552389	0.0158843	0.1302288	chr12	113588263	CCDC42B	113588263
286872	cg19439837	0.9459971	0.5527040	1.3392901	6.9655374	4.750562	4.5e-06	0.0455985	0.8339344	1.0000000	0.2005136	chr12	4923529	KCNA6;KCNA6	4923529
288096	cg19532212	0.7606680	0.4803455	1.0409904	4.4209486	5.359308	3.0e-07	0.0123746	2.2474246	0.1142103	0.1426619	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C	56769430
311691	cg21373263	0.8805707	0.5515533	1.2095881	3.2926911	5.285874	4.0e-07	0.0123746	2.0716919	0.1608692	0.1676110	chr10	126751982	CTBP2;CTBP2	126751982
322216	cg22240394	1.2229725	0.7670216	1.6789234	6.8239404	5.297489	4.0e-07	0.0123746	2.0993979	0.1524156	0.2325683	chr3	186211630		186211630
324251	cg22413938	-0.3880547	-0.5460152	-0.2300942	-4.5630336	-4.851858	2.9e-06	0.0335705	1.0632521	1.0000000	0.0797285	chr14	78447481		78447481
338217	cg23477849	0.3810081	0.2311925	0.5308237	4.8962493	5.022741	1.4e-06	0.0232259	1.4548453	0.5341954	0.0755056	chr19	5698492	LONP1	5698492
339781	cg23601521	0.7996758	0.4972086	1.1021431	4.8708259	5.221641	5.0e-07	0.0127085	1.9190935	0.2165310	0.1540110	chr2	50275179	NRXN1;NRXN1;NRXN1	50275179
370410	cg25954729	-0.3034838	-0.4163024	-0.1906653	-6.3724574	-5.312742	4.0e-07	0.0123746	2.1375974	0.1416105	0.0562146	chr11	66610784	RCE1;C11orf80;RCE1	66610784
379632	cg26608798	0.3969674	0.2358372	0.5580975	0.5750420	4.865660	2.7e-06	0.0334209	1.0945703	1.0000000	0.0813703	chr16	33853544		33853544
381104	cg26708724	0.9252394	0.5664932	1.2839856	6.7173655	5.093758	1.0e-06	0.0176594	1.6184667	0.3885072	0.1828323	chr4	187509785	FAT1	187509785
392164	cg27503275	0.4776627	0.2828083	0.6725171	4.1214740	4.841489	3.0e-06	0.0341627	1.0390945	1.0000000	0.0987864	chr6	3880016		3880016

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	70723226	70723386	0.0000000	160	0.0000000	0.0000026	2
10	121578136	121578639	0.0000000	503	0.0000000	0.0000012	4
14	78447480	78447640	0.0000000	160	0.0000000	0.0000126	3
19	50194119	50194252	0.0000000	133	0.0000000	0.0000160	5
4	186732836	186733060	0.0000000	224	0.0000000	0.0000130	7
4	24796918	24797176	0.0000000	258	0.0000000	0.0000182	6
14	76734326	76734605	0.0000000	279	0.0000000	0.0000220	5
21	45773781	45773997	0.0000000	216	0.0000000	0.0000374	2
5	135416204	135416613	0.0000000	409	0.0000000	0.0000256	9
11	63679431	63679637	0.0000001	206	0.0000001	0.0001231	2
20	62716331	62716606	0.0000001	275	0.0000001	0.0001330	4
17	78549323	78549371	0.0000001	48	0.0000002	0.0011147	3
5	1868136	1868357	0.0000004	221	0.0000005	0.0007368	4
22	45704987	45705042	0.0000015	55	0.0000017	0.0104801	4
5	176755392	176755449	0.0000127	57	0.0000135	0.0839213	2
2	88583556	88583805	0.0001042	249	0.0001042	0.1522101	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M/Zn_log2_manhattan_DMP_adj.png")